The Last Ship - Season III
by Titanic X
Summary: The Red Flu has been cured, but a new foe and a new strain of the virus threatens everything they have worked so hard for. Now Nathan James and his crew must take up arms to save the world once more. As the last line of defense, can they succeed before a warlord in China carries out their plans, and can they cure this new strain of the virus before it's too late?
1. Prelude

The Last Ship - Recap

 _Last time on_ The Last Ship

The world fell into chaos with a new strain of the flu. But it was not a normal case of the flu. This one... was a killer. Already 80% of the world's human population and 2/3 of the living vehicle population died from it, and the fate of all survivors rested on a single ship and his crew: USS Nathan James.

Teaming up with a pair of paleomicrobiologists, the crew and ship found themselves in a race against time to find a cure before the rest of the world's populations died off. Fighting against drug lords, rogue Russian admirals, and a corrupt government in Baltimore, they finally managed to find a cure, but at a cost. The emergence of the very thing they were fighting to prevent from happening in the first place: racial superiority.

With Baltimore finally liberated and a cure in the works, the ship retreated down to Norfolk to replenish and stock up with supplies. Two new crew members joined the ship, and Nathan found himself falling in love with Dr. Rachel Scott. However, things took a turn for the worse when a new foe showed themselves, and it soon became a fight to not only save the country, but prevent a cult of racial supremacists from taking hold in the last bastion of democracy on the planet. The fighting took them from New Orleans to the coasts of Florida, and finally they dealt a fatal blow to the ship used by the cultists.

After months of being on the front lines, the ship and his crew have returned to America to restore hope to the country, taking up residence within St. Louis, once dubbed Fortress V and commanded by Spray Krane, a former FBI plane turned military commander. With a new President and with a new mission, Nathan and his team have a big job ahead of them. But can they succeed, or will the Immunes finally rule the world...?

Find out in this next season of _The Last Ship_! Coming June 12th to a PC near you!


	2. Prologue

" _...shot through the chest... Need medi...w...!_ "

" _Bleeding out rapidly... to... spit...!_ "

" _Ambulance...y! Hold... lon...!_ "

" _Not sure how...keep...live!_ "

" _Do it, dammit!_ "

" _Hurry! Losing...!_ "

"... _Help on...way!_ "

" _Ambulance in... ge! Approaching...!_ "

" _Hurry!_ "

 _...Pain..._

 _Loss..._

 _Agony..._

 _His eyes were wide as he stared at the sight before him. The blood pooling around her... Her pale complexion, her glazed blue eyes, and her hair falling about her bare shoulders..._

 _The medics plunged into the hole created in her heart, using their best skills to try and suture the wound closed before it bled out. Her breathing was ragged, and her eyes slipped closed as they continued to work. The heartrate monitor set up to keep her heartbeat examined was starting to flatline. It was now a race against time. He watched as she was loaded onto the ambulance as soon as he skidded to a stop after careening around the corner. The hotel was a mass of every person and vehicle imaginable as they watched the world's savior dying before their very eyes. Some children of both man and machine were crying, and he felt a bit of sympathy because to be honest, he felt the same way..._

 _Tears streaked down his superstructure as he gazed at the ambulance's retreating shape, his siren wailing as loud as it could go. But it was nothing compared to the literal roar of rage, fury, and grief that escaped his throat, outpacing even the loudest sirens mankind had made..._

* * *

 _Across the globe, a new threat looms._

 _With the fate of the world in the balance,_

 _There is no choice..._

 _But to take up arms once more_

 _And defend what is right!_

* * *

 **(BGM: For The Win - Two Steps From Hell)**

(Scenes from the Last Ship start to play)

(Rachel Scott is shown as she looks back, a syringe filled with blue liquid behind her)

(Captain Tom Chandler hold his hat under one arm as his wife's spirit appears beside him, his family huddling up in front of his house in Norfolk)

(Mike Slattery narrows his eyes as he clenches his hands into fists, a golden police badge and naval ensign appearing behind him)

(Russell Jeter steps out of the shadows, an angelic figure appearing behind him as he looks at a cloudless blue sky)

(Danny Green holds a rifle in both hands, his dog Admiral Halsey right beside him, his wife's image appearing in the background along with their newborn son, Frankie)

(Kara Green stands beside the President of the United States, holding datapads and notes in her hands, Danny's image behind her and her son lying in a stroller)

(Andrea Garnett stands beside the engines of the ship, wearing her earplugs and taking notes before looking up)

(Alisha Granderson steps out of a hatch on board the ship, closing it as a torn up picture of her mother falls from her hands to be stepped on by another crewmember)

(Carlton Burke looks up from cleaning a gun in the helicopter's hangar)

(Eric Miller glances back over his shoulder as his other teammates join him)

(Wolf Taylor does a few martial arts moves against some thugs before landing and looking directly at the camera)

(Cameron Burk looks back from the bridge wing, his eyes landing on the distant skyline of Shanghai)

(Will Mason is shown lying on the ground, with blood coming from a gunshot wound, several shapes huddled around him)

(Cruz looks back with his gun at the ready, the coast of Vietnam in the background as the sun sets)

(Ray Diaz looks up from a comic book he is sketching, an image of the ship appearing behind him before it shifts to show him on board, a sketchbook in the background)

(O'Connor is shown deep within enemy clutches, his eyes blazing with hatred, a faint image of the destroyer within them)

(John "Gator" Meija is shown at a chart table, pointing out paths for them to go down as the ship is underway)

(Doc Rios is shown with five others huddled in a small cage, his eyes narrowed in anger)

(Carl Nishioka is shown in the CIC, speaking to the crew before he turns and heads over to his own station)

(Sasha Cooper is shown with Chandler beside her, a shadowy shape behind her)

(USS Nathan James is shown looking down at a picture of him and Rachel, his green eyes listless and his superstructure streaked with tears)

(President Michener is shown within the Courthouse of St. Louis, the Arch behind him with an American flag in the background)

(A shadowy form hovers over China before it moves over the camera, and a small glimmer of light appears)

(Japan is shown bathed in blood, a sinister shape behind it, as if grasping at it like a human hand)

(Nathan James and his crew is shown in front of the city of St. Louis with the series name above them)

* * *

The window was fogged by his breath, but he didn't care.

All he could see was her lying there in that hospital bed, an oxygen mask strapped to her face, her hair falling over her pale skin and the bandages wrapped tightly around her chest, stitches barely keeping the wound closed. A heart rate monitor checked her heartbeat, which was very, very weak due to the bullet penetrating and exiting cleanly.

It had taken the doctors eighteen hours to stitch the hole back together and get her on life support.

His very form seemed to tense as the heartbeats wavered before stabilizing. His eyes softened as tears pricked at them and he closed them, bowing his head ever so slightly.

How he wished he had been there to save her! Or at least gotten one of the crew to move in and act fast. It was by pure luck a single pitty had spotted the injured woman and gotten her to a hospital as fast as he could go. Even then it seemed like he would lose the woman he had come to love. And to be honest, just seeing her in this state was enough to make his stomach twist itself in knots. He shivered at the thought of losing her, and leaving their young one without a mother.

He recalled the first day they had met. True he had had a lover prior to her, but... when she died, he just... couldn't help himself. Both of them had fallen head over heels for one another, and he felt his teeth clench themselves as he shifted a bit. He hated being like this, unable to help her, and unable to do much himself.

For once in his life, he was helpless. He was totally helpless. In spite of all his power, speed, strength, and intelligence... he was as helpless as a newborn child. His entire arsenal... all his radar systems... everything... it couldn't do much to help her. It was as if Fate was toying with them, trying to see if they really did deserve to live together as husband and wife.

He felt the familiar sense of fury building deep within him and he gritted his teeth even tighter. If he kept this up, he would wind up causing himself to lose a tooth or two. And right now, he wished he was right there with her, holding her close, comforting her. But he couldn't. He just couldn't.

Because he wasn't even human.

This brilliant young woman had so much life... and had done amazing things. She didn't deserve to die like this, helpless, trapped in a hospital bed at one of the docks close by. She deserved to be living, spending time with him and their young son, who drifted close to him, nuzzling and cheeping with worry. He nuzzled the little one as he broke down crying, and in truth, he felt like crying himself. His green eyes shimmered with tears as he whispered softly to his son.

His massive grey hull acted like a barrier to the young shipling, his eyes closing as he cried himself to sleep. The destroyer gently picked up the shipling and placed him in his crib on the dock, using his bow to gently rock it. Light movements often worked for moving the crib, he mused as he started singing softly to his son.

He only hoped that she would make it through this...

For everyone's sake.

* * *

The city was a bustling place as people wandered across the streets, chatting with one another, hope finally returned to their eyes and minds. The cars and trucks passing by one another greeted each other on the road, and sometimes honked their horns in acknowledgement of the humans wandering the streets and sidewalks. A few helicopters and planes flew overhead, some of them doing minor stunts to liven up their commute from home to work. It often brought smiles to the children and they enjoyed it.

One such plane blasted past another older plane, startling him into dropping his mail cargo and he started swearing at the reckless youngster. The black cropduster mix just rolled his eyes and did a complete aileron roll, finally relieved that the last of the Immunes had been reconverted back to normal civilized people. Well, sort of. Sure they still had some trace thoughts of being Chosen left, but this... state... they had been in was largely negated. The black plane smiled a bit as he remembered the relief and joy the people of St. Louis had felt during the docking of the naval destroyer who had helped save the planet. The cure, or the Scott cure, as it was now known, was being distributed, and he was one of those who had been vaccinated, despite never having been in contact with the disease. Still, he was relieved he and his family were safe from harm.

His mind drifted back to more pressing matters and he gunned it a bit more, his engine revving within his slim airframe as he poured on the power.

Ever since he had been in St. Louis for a family vacation, he had been stranded there during the initial Outbreak, as it was now called by people across the nation, and during those first days, he had basically turned the entire city into a fortress, keeping the populace both safe and alive. He fought against both bandits and raiders, taking out infected with his fellow warriors and doing much damage to the Immunes as they came crawling forward, trying to take over the world. Thankfully, the city was well defended by that point as the Army, Marines, and Air Force vehicles that had been there took the brunt of the fighting. It also helped that the river kept the city well supplied with fresh water and fish. But it hadn't been him alone. A variety of others had come forward to help him manage the city, growing food, going green with wind and solar power, and just keeping the city's morale up.

By the time the war against the Immunes had ended, Spray Krane had become a well-known commander of a totally self-sufficient fortress, as well as striving to find a cure with the help of what few scientists remained within the city borders. And it was here that he had been inducted into the military as a commander, being given full authority over the city's military garrison.

And he was currently heading to a meeting with two of his staff.

The black plane flew down low, coming in hot as he approached the narrow stretch of roadway. A few vehicles and people darted to the side as he flared all his control surfaces to slow his speed down and he cut his engine at the same time as he applied his brakes. The effort culminated in him slowing down drastically and he hurried off the roadway down a wider path, finally spotting the human and pitty waiting for him.

"About time, sir," the pitty joked as he folded his tines.

"Hey! Blame it on my stupid alarm clock!" Spray shot back as he huffed. "Anyway, what's the deal?"

"We got trouble. It's stirring in Japan," the woman said as she held up a sheaf of paper and leafed through it. She pulled out a paper and held it up. "Something's wrong here."

Spray narrowed his brown eyes as he moved behind her and peered over her shoulder. His eyes widened though when he saw it was a map of Japan. And unlike the area maps he had previously seen, there were more red areas than blue or green. "What's happening?" he asked.

"Apparently, sir, the cure isn't working as well as they had hoped," the woman said as she returned the paper to her stack and faced him. "It's as if the virus has mutated or something..."

"Hold on. Dr. Scott originally said it couldn't mutate..." Spray mused, his eyes narrowing in suspicion. "So... what the hell is happening then? Why isn't the cure effective?"

"Try more like not working," the pitty muttered.

"Hold on! The cure's not even _working?!_ " Spray blurted, his flaps and ailerons bristling in shock.

"Denny's right, sir. It's not working... at all," the woman said seriously.

"Terry's got a point," Denny Wildman said as he looked at her.

Terry Wilken nodded. "And no matter what we do, it only gets worse."

"What's China doing?" Spray asked.

As a military commander and having helped defend the city during the Outbreak, he was considered a close member of the President's inner circle, a huge surprise for the rest of the group. But it proved to be a good choice, as Spray's experience with the Immunes helped round up the rest of the leaders, although some still eluded capture.

"They say that they're doing all that they can, but somehow I doubt it, sir," Terry remarked.

Spray hummed in thought before he looked up. "Well, keep an eye on the situation and inform me if anything changes."

They both saluted as one. "Yes, sir!" they said.

Spray's eyes drifted away from them for a moment, and they landed on the ship currently resting at dock, his green eyes listless and out of it. His hull was sort of... sagging... for lack of a better term, and his gun was pointed downwards toward his deck a bit more. His mast also seemed to be at a more raked angle than was normal.

Nathan James was depressed over his wife's condition. It also made him really unable to take care of their son, so a human couple had taken on the task of at least keeping an eye on the youth. While he was a growing little fellow, he was still very small, and he was able to fit inside their boathouse currently. It wouldn't be long before he hit his first growth spurt though.

"How's Nathan holding up?" The words slipped out of his mouth before he knew he even said them.

"Not so good, sir," Terry murmured as she gazed at the destroyer. "His wife, as you know, is still in a coma, and the prognosis isn't looking good. Doctors are saying she may remain in a coma for the rest of her life..."

"Even after everything they did to save her?" Spray asked.

Denny nodded. "Yeah. They did what they could, but it wasn't enough I guess..." the pitty muttered as his eyes softened. Spray frowned as he inched his way past his two staff members and over to the dock, eyeing the destroyer.

* * *

"Nathan..."

He didn't even twitch.

"Nathan...!"

Still no movement.

"USS NATHAN JAMES!"

His eyes snapped open and he literally yelped, his mooring lines snapping with the motion and he shot his gaze to the left, his eyes landing on the sleek shape of a smaller speedboat approaching. Her eyes were blazing with fury as she coasted to a stop mere inches from his bow. He had to admit she did have guts; not very many, both man or machine, got close to a guided missile destroyer's mouth.

"What is it, Clarice?" he groaned, sagging against his dock. The destroyer had finally finished having all his wounds and damage repaired, but while he was physically fine, it was the mental and emotional wounds that still gnawed at him. His bright green eyes were now dull and reflected very little of his passion for virology, his major in school and college. In fact, he displayed little to no emotion now since his wife had fallen into a coma six months ago after she was shot by an Immune. Nathan still swore revenge against the man, but so far no luck.

"It's about time you got your butt down to the dry dock for your physical," she said as she flicked one of her antennae in that direction.

Nathan sighed as he finally nipped his mooring lines and engaged his engines, making his way down to the dry dock for his annual physical. He didn't know why; he was perfectly healthy and healed now. But, who was he to argue with the woman placed in charge of his recovery and rehabilitation? Dr. Clarice Waveston was a ship doctor, which was ironic considering how she was a speedboat of all things. But he figured it kind of made sense as she could check him when out on the water. But if that were the case, why was he to go into dry dock?

He brushed it aside as he made his way into the dock further down the mighty Mississippi River and allowed them to close the dock doors and start draining the water. He felt the cold rush of air as it brushed against his hull, all the way down to his keel. He could spot a few divers moving about as he adjusted his position a bit, feeling them wedging the support blocks along his keel, aligning them with his frame to fully support his weight.

Once the water was fully drained, he shivered due to the lack of warmth on his underside. Sure he could take it, but it still made him shudder.

He closed his eyes as the exam finally commenced. Everything just seemed so mechanical now. He did whatever he was asked, opening his mouth, flexing his rudder and spinning his props to make sure they worked. He allowed them to check his hearing and eyesight, and as usual, he had a perfect bill of health. Yet he felt them poking and prodding on his keel, examining it to make sure he lacked any damage from his fight against Achilles and the Immune captains who took control of her. His mind was numb as they finished up what seemed to be hours later. As the dock flooded again, he looked back at where his wife lay. It didn't take very long, and soon he was excused to leave. He moved closer to the building set up as a hospital and peered inside.

He still could not accept that she could possibly remain in a coma for the rest of her life. And truth was, he was actually being kind of selfish, but he didn't even realize it until much, much later. He just wanted her to stay with him. But at the same time, he wanted to let her pass on. Yet, as long as she still breathed, she could be alive. And that was why he refused to pull the plug on Rachel Scott's life support.

He spotted movement out of the corner of his eye and he looked over to see Spray Krane huddling behind some crates. He sighed. Great. Now he had to deal with the base commander.

"What is it, sir?" he asked in a depressed tone.

Spray yelped a bit and backpedaled before he regained himself and rolled up to the destroyer. "Nathan, you're not...you okay?" he asked.

"Why would I be?" he muttered lowly. "My wife's in a coma, and... I just don't know what I'll do if she dies..." He finally closed his eyes and now the black plane could see that this was taking a very severe toll on him. He had dark spots under his eyes and he looked like he hadn't slept in weeks.

For once, Spray actually felt sorry for him. To nearly lose his wife and then not know if she would live or die... It was a fate he did not want to wish on anyone, even those Immunes. He rolled closer and placed his nose on his hull briefly. "She'll be okay... She's been through worse..." he muttered, feeling his eyes prick with tears.

"I doubt it..." Nathan muttered darkly. He snorted a bit, pushing the plane back by the force of his breath; Spray reeled in disgust: Nathan hadn't even gotten his teeth cleaned in the last few months.

"Nathan, please. You're not gonna do her any good just moping and letting yourself waste away like this. I mean, come on! You haven't even had your teeth cleaned for weeks! When she wakes up, she's gonna be very disappointed in you!" Spray snapped as he backed up a bit more. "I know I am, and I'm not even your commanding officer!"

"You mean _if_ she wakes up..." the ship muttered. "The doctors said she may never wake up again..."

"She will, Nathan," Spray tried to assure him. But the destroyer just sighed and closed his eyes, his sides shaking a bit.

"I doubt it. The doctors were pretty adamant about it," he whispered, his voice wavering. "I... I don't know what I'd do without her..."

Spray felt a pang of sympathy within his engine and heart and he inched closer again. "Nathan..."

"Just go. I... I need to be left alone..." Nathan muttered, finally tuning out all further attempts at communication.

The black FBI plane blinked, but acknowledged that he needed space and backed up, heading back down the street towards his office and headquarters.

As he passed by other inhabitants of the city, he gave a few waves, but for the most part his body was on autopilot. His mind was too busy pondering the situation in Asia. It just didn't seem right for the virus to have shifted and mutated. How was that even possible? It was supposed to be stable and able to be defeated with the cure. So then why wasn't it working?

Unless there was another factor involved somehow...

He recalled Niels Sørensen, or as Rachel had called him, Patient Zero, and the plane shuddered against his will. From the description of the guy, he sounded like a leech. Brilliant, but very leechlike in his behavior regarding Rachel. Trying to murder her shipling was another matter, and Spray gritted his teeth at the mere thought. ' _Had it been one of my kids... I'm not sure I would've held back..._ ' he thought to himself.

Spray remembered that somehow he had bonded his DNA to the virus and made it stable. But then Rachel had removed it and killed him, along with his combination sequence. So, then what was happening to the virus? Without Niels' recombination sequence, it was impossible to alter the virus and weaponize it. But what if someone else had? That was a far flung possibility as the creator was now dead. But it was still out there, and he had to keep an open mind. Well, it helped that his little... predicament... was what also helped. He wasn't actually a true plane by birth, but a freak accident involving a dose of ship serum and two different plane breeds' oil seeping into his bloodstream led to him becoming a plane when he was seventeen years old. Thankfully, no one else had been around, except his three best friends who had also undergone the same freak accident along with his parents, and their families as well. He still wasn't sure how it had truly happened to all of them, but it had.

So now he had to keep his true past a secret for fear of someone doing experimenting on him and his friends and loved ones. Or even trying to do it themselves. And that was the last thing the world needed right now.

He finally arrived at his office, or in reality, his hangar. He nudged open the heavy doors and made his way inside before he closed them and the thick steel blast doors slid shut. The FBI agent made his way into his office and booted up his terminal, logging into the database he had compiled in recent months on the situation and the reports on the mission to find the cure. His eyes were hard as he scanned them over, reading the reports Rachel had made up on Niels' efforts and work. While most of it flew over his head, he did get the basic idea, and he skimmed the more "dumbed down" version.

Of course, it was still impossible, at least according to the data Rachel had provided prior to her near-death assassination.

So then what was really happening in Japan?

He was so focused he had no idea his comm was beeping.

At least until a voice caught him off guard.

" _She's woken up, sir! Dr. Rachel Scott has come out of her coma...!_ "


End file.
